We use particulate questions to investigate the mental association between the concepts of molecule and compound in chemistry students with different levels of academic preparation. We focus our analysis on the answers that undergraduate and graduate students provided when asked to classify a substance such as A2 (represented in particulate form) as element, compound, or mixture. Our results indicate that a significant proportion of students misclassified molecular elements as chemical compounds. Surprisingly, the mental association between the concepts of molecule and compound was stronger in students with higher levels of preparation. Advanced students seemed to differentiate between elements and compounds using an alternative classification system based on molecular structure rather than on chemical composition. Even some chemistry faculty had working definitions of element and compound that did not match the definitions conventionally included in chemistry textbooks.